Genetically engineered corn and soybeans make it easy for farmers to eradicate weeds, including the long-lived and unruly milkweed.

But they might be putting the monarch butterfly in peril.

The rapid spread of herbicide-resistant crops has coincided with — and may explain — the dramatic decline in monarch numbers that has troubled some naturalists over the past decade, according to a new study by researchers at the University of Minnesota and Iowa State University.

Between 1999 and 2010, the same period in which so-called GMO crops became the norm for farmers, the number of monarch eggs declined by an estimated 81 percent across the Midwest, the researchers say. That’s because milkweed — the host plant for the eggs and caterpillars produced by one of one of the most gaudy and widely recognized of all North American butterflies — has nearly disappeared from farm fields, they found.

It is one of the clearest examples yet of unintended consequences from the widespread use of genetically modified seeds, said John Pleasants, a monarch researcher from Iowa State in Ames, Iowa.

“When we put something out there, we don’t know always what the consequences are,” he said.

Pleasants and Karen Oberhauser, of the University of Minnesota, published their findings online last week in the journal Insect Conservation and Diversity.

“It is quite an extraordinary paper,” said Chip Taylor, an insect ecologist at the University of Kansas and the director of research at Monarch Watch, a conservation group. He noted that Oberhauser and Pleasants were able to tie the loss of habitat to a decline in numbers across the country.

But the evidence they present — estimates of the number of milkweed plants across the Corn Belt and a decade’s worth of butterfly egg counts by an army of volunteer citizens — is indirect, say others.

“It does not resolve the debate,” said Leslie Ries, a University of Maryland professor who studies monarchs.

Butterflies in decline

The orange and black butterflies migrate every year to the mountains of Mexico, where they collect in fluttering clouds in trees, an extraordinary event that has inspired festivals and tourism.

But for reasons that are not well understood, the number of butterflies that make it to Mexico — half of which come from the Midwest — has been on the decline. This year, according to a report released Thursday, the butterflies occupied seven acres of trees in their refuge west of Mexico City — 28 percent less than last year and a fraction of the 45 acres they occupied in 1996, a peak year.

Experts said last year’s drought probably had a serious effect on the insects. Others say damage to the wintering grounds from logging and development are also playing a part, and that the number that make it to Mexico does not necessarily reflect the health of the species.

But some scientists have for years wondered whether the use of genetically modified crops is affecting the spring and summer reproduction in this country.

Earlier studies suggested that monarch caterpillars would die if they ate milkweed dusted with pollen from another kind of engineered seed known as BT corn. It contains a gene that produces a toxin that kills corn-eating pests.

That theory was disproved, but it led scientists to take a hard look at milkweed plants in corn and soybean fields, said Pleasants. “Surprisingly, monarchs use those milkweeds more heavily than milkweed outside [farm fields],” he said. The butterflies lay nearly four times as many eggs on farm field plants as on those in pastures or on roadsides, the researchers said.

More important, they also found “that milkweed in the fields was disappearing,” he said. That’s because more farmers are using a new kind of genetically modified seed developed by Monsanto, Roundup-ready corn and soybeans, that contain a gene allowing the plants to withstand Roundup, or glyphosate. That allows farmers to spray their fields without harming the crop.

Monsanto, which did not respond to a request for comment, says on its website the seeds help farmers increase yield. Today, it’s used by 94 percent of soybean farmers and 72 percent of corn farmers, according to federal data.

Assessing the effect on milkweed plants both in and out of farm fields, was difficult, researchers said — never mind the challenge of counting butterfly eggs.

Pleasants said he used data on the change in milkweed density in Iowa, and extrapolated those numbers to landscape use data across the Midwest. That showed an estimated 58 percent decline in milkweed plants throughout the Corn Belt, primarily on agricultural lands.

Oberhauser supplied data she has been collecting for years through the Monarch Larva Monitoring Project. Every week during the monarch breeding season, volunteers across the country go to the same patches of non-agricultural milkweed in their communities and count all the eggs they can find.

That showed two things: Butterflies were not flocking to breed on plants outside agricultural fields; those numbers remained the same. And overall production, measured in eggs, declined 81 percent between 1999 and 2010.

Taylor said the new study should help make the case that increasing monarch habitat along roads in pastures, gardens and on conservation lands must become a national priority because the milkweed will never come back to farm fields, he said.

“The scale of the loss of habitat is so big that unless we compensate for it in some way, the population will decline to the point where it will disappear,” he said.